This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling. More...
#include <SimpleThreadingMover.hh>
Public Member Functions | |
| SimpleThreadingMover ()=default | |
| Default constructor. More... | |
| SimpleThreadingMover (std::string thread_sequence, core::Size start_position) | |
| Initialization constructor. More... | |
| SimpleThreadingMover (SimpleThreadingMover const &)=default | |
| Default copy constructor. More... | |
| ~SimpleThreadingMover () override | |
| Destructor. More... | |
| void | set_sequence (std::string thread_sequence, core::Size start_position) |
| Set the sequence to thread onto the structure used in apply and where to start. More... | |
| void | set_pack_neighbors (bool pack_neighbors) |
| Pack the neighbor residues? More... | |
| void | set_neighbor_distance (core::Real neighbor_dis) |
| Set the packing distance for neighbor pack. More... | |
| void | set_sequence_mode (std::string const &mode_string_in) |
| Set the sequence mode, by string. More... | |
| void | set_sequence_mode (core::simple_metrics::metrics::SequenceMetricMode const mode_in) |
| Set the sequence mode, by enum. More... | |
| bool | get_pack_neighbors () const |
| core::Real | get_neighbor_distance () const |
| core::simple_metrics::metrics::SequenceMetricMode | sequence_mode () const |
| Get the sequence mode. More... | |
| void | set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn) |
| Set the scorefunction used for packing. More... | |
| void | set_pack_rounds (core::Size pack_rounds) |
| Set the number of pack rounds. More... | |
| void | set_skip_unknown_mutant (bool const setting) |
| Set whether we skip unknown residue types, or throw errors. More... | |
| bool | skip_unknown_mutant () const |
| Get whether we skip unknown residue types, or throw errors. More... | |
| void | apply (core::pose::Pose &pose) override |
| Main Method. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| protocols::moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Private Member Functions | |
| std::map< core::Size, std::string > | determine_mutations (core::Size const start_position, std::string const &sequence, core::simple_metrics::metrics::SequenceMetricMode const mode, core::pose::Pose const &pose) const |
| Given the sequence, the interpretation mode, and the start position, fill a map of position->mutation name. More... | |
| std::map< core::Size, std::string > | determine_mutations_oneletter (core::Size const start_position, std::string const &sequence) const |
| Given the sequence as one-letter codes and the start position, fill a map of position->mutation name. More... | |
| std::map< core::Size, std::string > | determine_mutations_comma_separated (core::Size const start_position, std::string const &sequence, core::simple_metrics::metrics::SequenceMetricMode const mode, core::pose::Pose const &pose) const |
| Given the sequence as a comma-separated list of either three-letter codes, base names, or full names, plus the start position, fill a map of position->mutation name. More... | |
Private Attributes | |
| core::Size | start_position_ = 1 |
| std::string | thread_sequence_ = "0" |
| bool | pack_neighbors_ = false |
| core::Real | neighbor_dis_ = 6.0 |
| core::scoring::ScoreFunctionCOP | scorefxn_ = nullptr |
| std::string | parsed_position_ = "NA" |
| bool | skip_unknown_mutant_ = false |
| core::Size | pack_rounds_ = 5 |
| core::simple_metrics::metrics::SequenceMetricMode | sequence_mode_ = core::simple_metrics::metrics::SequenceMetricMode::ONELETTER_CODE |
| How should the sequence be interpreted? Default is as a string of one-letter codes. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Detailed Description
This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling.
It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step. A sequence is just a string, additional '-' charactors denote to skip this position in the thread. Default is 5 rounds of packing.
Constructor & Destructor Documentation
◆ SimpleThreadingMover() [1/3]
|
default |
Default constructor.
◆ SimpleThreadingMover() [2/3]
| protocols::simple_moves::SimpleThreadingMover::SimpleThreadingMover | ( | std::string | thread_sequence, |
| core::Size | start_position | ||
| ) |
Initialization constructor.
◆ SimpleThreadingMover() [3/3]
|
default |
Default copy constructor.
◆ ~SimpleThreadingMover()
|
overridedefault |
Destructor.
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::simple_moves::MutateResidue::apply(), determine_mutations(), core::scoring::get_score_function(), neighbor_dis_, pack_neighbors_, pack_rounds_, core::pose::parse_resnum(), parsed_position_, scorefxn_, sequence_mode_, start_position_, core::chemical::orbitals::strip_whitespace(), thread_sequence_, core::id::to_string(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
◆ determine_mutations()
|
private |
Given the sequence, the interpretation mode, and the start position, fill a map of position->mutation name.
References determine_mutations_comma_separated(), and determine_mutations_oneletter().
Referenced by apply().
◆ determine_mutations_comma_separated()
|
private |
Given the sequence as a comma-separated list of either three-letter codes, base names, or full names, plus the start position, fill a map of position->mutation name.
References core::simple_metrics::metrics::BASE_NAME, core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeFinder::name3(), core::chemical::ResidueTypeFinder::patch_names(), core::chemical::ResidueTypeFinder::residue_base_name(), core::pose::Pose::residue_type_set_for_pose(), skip_unknown_mutant_, core::simple_metrics::metrics::THREELETTER_CODE, and protocols::simple_moves::TR().
Referenced by determine_mutations().
◆ determine_mutations_oneletter()
|
private |
Given the sequence as one-letter codes and the start position, fill a map of position->mutation name.
Given the as one-letter codes and the start position, fill a map of position->mutation name.
Supports possibility of positions of the form X[NCAA_NAME].
References core::chemical::aa_from_oneletter_code(), core::chemical::name_from_aa(), core::chemical::oneletter_code_specifies_aa(), skip_unknown_mutant_, and protocols::simple_moves::TR().
Referenced by determine_mutations().
◆ fresh_instance()
|
overridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_neighbor_distance()
| core::Real protocols::simple_moves::SimpleThreadingMover::get_neighbor_distance | ( | ) | const |
References neighbor_dis_.
◆ get_pack_neighbors()
| bool protocols::simple_moves::SimpleThreadingMover::get_pack_neighbors | ( | ) | const |
References pack_neighbors_.
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References neighbor_dis_, pack_neighbors_, pack_rounds_, core::scoring::parse_score_function(), parsed_position_, scorefxn_, set_sequence_mode(), skip_unknown_mutant_, and thread_sequence_.
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from protocols::moves::Mover.
References mover_name().
Referenced by protocols::protein_mpnn::ProteinMPNNMover::provide_citation_info().
◆ provide_xml_schema()
|
static |
◆ sequence_mode()
|
inline |
Get the sequence mode.
References sequence_mode_.
◆ set_neighbor_distance()
| void protocols::simple_moves::SimpleThreadingMover::set_neighbor_distance | ( | core::Real | neighbor_dis | ) |
Set the packing distance for neighbor pack.
References neighbor_dis_.
◆ set_pack_neighbors()
| void protocols::simple_moves::SimpleThreadingMover::set_pack_neighbors | ( | bool | pack_neighbors | ) |
Pack the neighbor residues?
References pack_neighbors_.
◆ set_pack_rounds()
| void protocols::simple_moves::SimpleThreadingMover::set_pack_rounds | ( | core::Size | pack_rounds | ) |
Set the number of pack rounds.
References pack_rounds_.
◆ set_scorefxn()
| void protocols::simple_moves::SimpleThreadingMover::set_scorefxn | ( | core::scoring::ScoreFunctionCOP | scorefxn | ) |
Set the scorefunction used for packing.
References scorefxn_.
◆ set_sequence()
| void protocols::simple_moves::SimpleThreadingMover::set_sequence | ( | std::string | thread_sequence, |
| core::Size | start_position | ||
| ) |
Set the sequence to thread onto the structure used in apply and where to start.
Can have '-' charactors in sequence to denote a gap in the threaded sequence.
References start_position_, and thread_sequence_.
◆ set_sequence_mode() [1/2]
| void protocols::simple_moves::SimpleThreadingMover::set_sequence_mode | ( | core::simple_metrics::metrics::SequenceMetricMode const | mode_in | ) |
Set the sequence mode, by enum.
This determines how the sequence is interpreted (one-letter codes, three-letter codes, etc.).
References core::simple_metrics::metrics::END_OF_LIST, and sequence_mode_.
◆ set_sequence_mode() [2/2]
| void protocols::simple_moves::SimpleThreadingMover::set_sequence_mode | ( | std::string const & | mode_string_in | ) |
Set the sequence mode, by string.
This determines how the sequence is interpreted (one-letter codes, three-letter codes, etc.).
Referenced by parse_my_tag().
◆ set_skip_unknown_mutant()
|
inline |
Set whether we skip unknown residue types, or throw errors.
References skip_unknown_mutant_.
◆ skip_unknown_mutant()
|
inline |
Get whether we skip unknown residue types, or throw errors.
References skip_unknown_mutant_.
Member Data Documentation
◆ neighbor_dis_
|
private |
Referenced by apply(), get_neighbor_distance(), parse_my_tag(), and set_neighbor_distance().
◆ pack_neighbors_
|
private |
Referenced by apply(), get_pack_neighbors(), parse_my_tag(), and set_pack_neighbors().
◆ pack_rounds_
|
private |
Referenced by apply(), parse_my_tag(), and set_pack_rounds().
◆ parsed_position_
|
private |
Referenced by apply(), and parse_my_tag().
◆ scorefxn_
|
private |
Referenced by apply(), parse_my_tag(), and set_scorefxn().
◆ sequence_mode_
|
private |
How should the sequence be interpreted? Default is as a string of one-letter codes.
Referenced by apply(), sequence_mode(), and set_sequence_mode().
◆ skip_unknown_mutant_
|
private |
◆ start_position_
|
private |
Referenced by apply(), and set_sequence().
◆ thread_sequence_
|
private |
Referenced by apply(), parse_my_tag(), and set_sequence().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/SimpleThreadingMover.hh
- src/protocols/simple_moves/SimpleThreadingMover.cc
